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Personal profile

Research Interests

I was one of the first students to obtain an undergraduate degree in Bioinformatics and Computational Biology at University of Toronto. Then, I trained as a computational biologist at Duke University (PhD) under Drs. Greg Crawford and Terry Furey focusing on gene regulation, specifically, using high-throughput sequencing assays to study chromatin dynamics across diverse human cell lines. For my postdoc, I joined Ido Amit's lab in Immunogenomics at the Weizmann Institute of Science in Israel where I applied genomic approaches to the study of immunology. My landmark paper showed that tissue-resident macrophages are capable of adopting tissue-specific functions by reprogramming their chromatin landscape in response to signal from the local environment.

As a computational immunologist, I interested in mapping the gene regulatory networks of immune cells in health and disease, particularly macrophages in rheumatic disease. As a plastic immune cell type, macrophages are found throughout the body where they play an important role in both homeostatic functions and immune response. The are critical to the pathogenesis of autoimmune diseases, such as rheumatoid arthritis and systemic sclerosis. Using high-throughput sequencing assays and computational techniques, I seek to profile the transcriptional and epigenomic profile of macrophages in different tissues in mouse models and patients with these diseases. We believe that a better understanding of the function and malfunction of macrophages we enable to develop more precise and effective treatments.

Education/Academic qualification

PhD, Duke University

… → 2013

Research interests

  • Arthritis - Rheumatoid
  • Big Data
  • Bioinformatics
  • Chromatin
  • Computational Biology
  • Epigenetics
  • Gene Regulation
  • Genomics
  • Immunology
  • Rheumatology
  • Scleroderma
  • Systems Biology

Fingerprint Dive into the research topics where Deborah Rachelle Winter is active. These topic labels come from the works of this person. Together they form a unique fingerprint.

  • 7 Similar Profiles
Chromatin Medicine & Life Sciences
Macrophages Medicine & Life Sciences
Nucleosomes Medicine & Life Sciences
Genes Chemical Compounds
Single-Cell Analysis Medicine & Life Sciences
Histone Code Medicine & Life Sciences
Encyclopedias Medicine & Life Sciences
RNA Sequence Analysis Medicine & Life Sciences

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Grants 2017 2023

Macrophages
Skin
Skin Diseases
Mycophenolic Acid
Biopsy
Plasminogen Activator Inhibitor 1
Fibrosis
Mutation
Cardiomyopathies
Cardiac Myocytes
Reperfusion Injury
Infarction
Macrophages
Myocardial Reperfusion Injury
Myocardial Infarction
Epigenomics
Monocytes
Myeloid Cells
Chromatin
Inflammation

Research Output 2007 2019

  • 11877 Citations
  • 24 Article
  • 4 Review article
  • 2 Short survey
  • 1 Comment/debate
1 Citation (Scopus)

Lipocalin-2 is a pathogenic determinant and biomarker of neuropsychiatric lupus

Mike, E. V., Makinde, H. M., Gulinello, M., Vanarsa, K., Herlitz, L., Gadhvi, G., Winter, D. R., Mohan, C., Hanly, J. G., Mok, C. C., Cuda, C. M. & Putterman, C., Jan 1 2019, In : Journal of Autoimmunity. 96, p. 59-73 15 p.

Research output: Contribution to journalArticle

Biomarkers
Brain
RNA Sequence Analysis
Lipocalin-2
Memory Disorders
11 Citations (Scopus)

Single-cell transcriptomic analysis of human lung provides insights into the pathobiology of pulmonary fibrosis

Reyfman, P. A., Walter, J. M., Joshi, N., Anekalla, K. R., McQuattie-Pimentel, A. C., Chiu, S., Fernandez, R., Akbarpour, M., Chen, C. I., Ren, Z., Verma, R., Abdala-Valencia, H., Nam, K., Chi, M., Han, S. H., Gonzalez-Gonzalez, F. J., Soberanes, S., Watanabe, S., Williams, K. J. N., Flozak, A. S. & 29 others, Nicholson, T. T., Morgan, V. K., Winter, D. R., Hinchcliff, M., Hrusch, C. L., Guzy, R. D., Bonham, C. A., Sperling, A. I., Bag, R., Hamanaka, R. B., Mutlu, G. M., Yeldandi, A. V., Marshall, S. A., Shilatifard, A., Amaral, L. A. N., Perlman, H. R., Sznajder, J. I., Christine Argento, A., Gillespie, C. T., Dematte, J., Jain, M., Singer, B., Ridge, K. M., Lam, A. P., Bharat, A., Bhorade, S. M., Gottardi, C., Budinger, GR. S. & Misharin, A., Jun 15 2019, In : American journal of respiratory and critical care medicine. 199, 12, p. 1517-1536 20 p.

Research output: Contribution to journalArticle

Open Access
Single-Cell Analysis
Pulmonary Fibrosis
Lung
RNA Sequence Analysis
Alveolar Macrophages
2 Citations (Scopus)

A beginner’s guide to analysis of RNA sequencing data

Koch, C. M., Chiu, S. F., Akbarpour, M., Bharat, A., Ridge, K. M., Bartom, E. T. & Winter, D. R., Aug 1 2018, In : American journal of respiratory cell and molecular biology. 59, 2, p. 145-157 13 p.

Research output: Contribution to journalReview article

RNA Sequence Analysis
RNA
Publications
Research Personnel
Bioinformatics
4 Citations (Scopus)

Neuropsychiatric Systemic Lupus Erythematosus Is Dependent on Sphingosine-1-Phosphate Signaling

Mike, E. V., Makinde, H. M., Der, E., Stock, A., Gulinello, M., Gadhvi, G. T., Winter, D. R., Cuda, C. M. & Putterman, C., Jan 1 2018, In : Frontiers in immunology. 9, 1 p.

Research output: Contribution to journalArticle

Central Nervous System Lupus Vasculitis
Inbred MRL lpr Mouse
Lysosphingolipid Receptors
Cytokines
Brain

Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis

Reyfman, P. A., Walter, J. M., Joshi, N., Anekalla, K. R., McQuattie-Pimentel, A. C., Chiu, S., Fernandez, R., Akbarpour, M., Chen, C-I., Ren, Z., Verma, R., Abdala-Valencia, H., Nam, K., Chi, M., Han, S., Gonzalez-Gonzalez, F. J., Soberanes, S., Watanabe, S., Williams, K. J. N., Flozak, A. S. & 29 others, Nicholson, T. T., Morgan, V. K., Winter, D. R., Hinchcliff, M., Hrusch, C. L., Guzy, R. D., Bonham, C. A., Sperling, A. I., Bag, R., Hamanaka, R. B., Mutlu, G. M., Yeldandi, A. V., Marshall, S. A., Shilatifard, A., Amaral, L. A. N., Perlman, H., Sznajder, J. I., Argento, A. C., Gillespie, C. T., Dematte, J., Jain, M., Singer, B. D., Ridge, K. M., Lam, A. P., Bharat, A., Bhorade, S. M., Gottardi, C. J., Budinger, G. R. S. & Misharin, A. V., Dec 15 2018, In : American Journal of Respiratory and Critical Care Medicine.

Research output: Contribution to journalArticle

Single-Cell Analysis
Pulmonary Fibrosis
Lung
RNA Sequence Analysis
Alveolar Macrophages